It's a mystery (and a misery) to me, as well. Being an ancient Windows user (I'm the ancient one, not Windows) I often find myself puzzled about navigating and using apps on the iPad. But for the most part I put it down to my ingrained expectations about how things should work. Took me quite awhile to understand that Apple doesn't believe I should be concerned about where files are located or be able to access the same file with different apps, for example. And I still chafe over the fact that I cannot simply open another app on the screen in another resizable window. And why can't I create multiple user "accounts" with different permissions on my iPad? Ahh...so many (admittedly not major) frustrations. But I've adjusted for the most part. I just content myself with the restrictions Apple imposes on me and enjoy the benefits.
iTunes and the App Store are different. One is a now ancient application designed for one purpose with functionality layered on top of it with no thought as to the vast differences in the devices it's supposed to support. The other is simply an atrociously designed app with so little functionality as to be infuriating. Why are there no standards for what constitutes a true "iPad" app? Must we rely on the often violated convention to stick "HD" somewhere in the title of an app? Is the meaning of an "iOS" app supposed to be that it runs equally well or equally badly on an iPhone and an iPad? When my search results generate 200 apps do I really have to begin at the beginning of the list every time I return from examining an app?
The very existence of App Shopper suggests just how bad the App Store is.